Hana-Kimi centers on Mizuki Ashiya, a Japanese girl who lives in the United States. One day, she sees a track and field competition on TV, and becomes attracted to one of the competitors, Izumi Sano, competing in the high jump.

She begins to idolize the young athlete and eventually transfers to Japan to attend the same school that Sano attends. There is a catch, however… Sano attends an all-boys high school, named Osaka Gakuen, and Mizuki must disguise herself as a boy to enter.